Ensembl Tools. EBI is an Outstation of the European Molecular Biology Laboratory.
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1 Ensembl Tools EBI is an Outstation of the European Molecular Biology Laboratory.
2 Questions? We ve muted all the mics Ask questions in the Chat box in the webinar interface I will check the Chat box periodically for questions There s no threading so please respond
3 Objectives What is Ensembl? What tools are available in Ensembl? How to use the online tools in Ensembl. Where to go for help and documentation.
4 Overview Introduction to Ensembl BLAST/BLAT Sequence searching Assembly Converter Convert files between genome assemblies Data Slicer Pull out sections of VCF and BAM files File Chameleon Custom download of reference files for NGS analysis Variant Effect Predictor (VEP) Analyse your own variants
5 Introduction Why do we need genome browsers? 1977: 1st genome to be sequenced (5 kb) 2004: finished human sequence (3 Gb)
6 CGGCCTTTGGGCTCCGCCTTCAGCTCAAGACTTAACTTCCCTCCCAGCTGTCCCAGATGACGCCATCTGAAATTTCTTGGAA ACACGATCACTTTAACGGAATATTGCTGTTTTGGGGAAGTGTTTTACAGCTGCTGGGCACGCTGTATTTGCCTTACTTAAGC CCCTGGTAATTGCTGTATTCCGAAGACATGCTGATGGGAATTACCAGGCGGCGTTGGTCTCTAACTGGAGCCCTCTGTCCCC ACTAGCCACGCGTCACTGGTTAGCGTGATTGAAACTAAATCGTATGAAAATCCTCTTCTCTAGTCGCACTAGCCACGTTTCG AGTGCTTAATGTGGCTAGTGGCACCGGTTTGGACAGCACAGCTGTAAAATGTTCCCATCCTCACAGTAAGCTGTTACCGTTC CAGGAGATGGGACTGAATTAGAATTCAAACAAATTTTCCAGCGCTTCTGAGTTTTACCTCAGTCACATAATAAGGAATGCAT CCCTGTGTAAGTGCATTTTGGTCTTCTGTTTTGCAGACTTATTTACCAAGCATTGGAGGAATATCGTAGGTAAAAATGCCTA TTGGATCCAAAGAGAGGCCAACATTTTTTGAAATTTTTAAGACACGCTGCAACAAAGCAGGTATTGACAAATTTTATATAAC TTTATAAATTACACCGAGAAAGTGTTTTCTAAAAAATGCTTGCTAAAAACCCAGTACGTCACAGTGTTGCTTAGAACCATAA ACTGTTCCTTATGTGTGTATAAATCCAGTTAACAACATAATCATCGTTTGCAGGTTAACCACATGATAAATATAGAACGTCT AGTGGATAAAGAGGAAACTGGCCCCTTGACTAGCAGTAGGAACAATTACTAACAAATCAGAAGCATTAATGTTACTTTATGG CAGAAGTTGTCCAACTTTTTGGTTTCAGTACTCCTTATACTCTTAAAAATGATCTAGGACCCCCGGAGTGCTTTTGTTTATG TAGCTTACCATATTAGAAATTTAAAACTAAGAATTTAAGGCTGGGCGTGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGA GGCCGAGGTGGGCGGATCACTTGAGGCCAGAAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCCTATCTCTACTAAAAAT ACAAAAAATGTGCTGCGTGTGGTGGTGCGTGCCTGTAATCCCAGCTACACGGGAGGTGGAGGCAGGAGAATCGCTTGAACCC TGGAGGCAGAGGTTGCAGTGAGCCAAGATCATGCCACTGCACTCTAGCCTGGGCCACATAGCATGACTCTGTCTCAAAACAA ACAAACAAACAAAAAACTAAGAATTTAAAGTTAATTTACTTAAAAATAATGAAAGCTAACCCATTGCATATTATCACAACAT TCTTAGGAAAAATAACTTTTTGAAAACAAGTGAGTGGAATAGTTTTTACATTTTTGCAGTTCTCTTTAATGTCTGGCTAAAT AGAGATAGCTGGATTCACTTATCTGTGTCTAATCTGTTATTTTGGTAGAAGTATGTGAAAAAAAATTAACCTCACGTTGAAA AAAGGAATATTTTAATAGTTTTCAGTTACTTTTTGGTATTTTTCCTTGTACTTTGCATAGATTTTTCAAAGATCTAATAGAT ATACCATAGGTCTTTCCCATGTCGCAACATCATGCAGTGATTATTTGGAAGATAGTGGTGTTCTGAATTATACAAAGTTTCC AAATATTGATAAATTGCATTAAACTATTTTAAAAATCTCATTCATTAATACCACCATGGATGTCAGAAAAGTCTTTTAAGAT TGGGTAGAAATGAGCCACTGGAAATTCTAATTTTCATTTGAAAGTTCACATTTTGTCATTGACAACAAACTGTTTTCCTTGC AGCAACAAGATCACTTCATTGATTTGTGAGAAAATGTCTACCAAATTATTTAAGTTGAAATAACTTTGTCAGCTGTTCTTTC AAGTAAAAATGACTTTTCATTGAAAAAATTGCTTGTTCAGATCACAGCTCAACATGAGTGCTTTTCTAGGCAGTATTGTACT TCAGTATGCAGAAGTGCTTTATGTATGCTTCCTATTTTGTCAGAGATTATTAAAAGAAGTGCTAAAGCATTGAGCTTCGAAA TTAATTTTTACTGCTTCATTAGGACATTCTTACATTAAACTGGCATTATTATTACTATTATTTTTAACAAGGACACTCAGTG GTAAGGAATATAATGGCTACTAGTATTAGTTTGGTGCCACTGCCATAACTCATGCAAATGTGCCAGCAGTTTTACCCAGCAT CATCTTTGCACTGTTGATACAAATGTCAACATCATGAAAAAGGGTTGAAAAAAGGAATATTTTAATAGTTTTCAGTTACTTT
7 We need to make the data mean something nih.gov/mapview ensembl.org
8 Ensembl Features Gene builds for ~70 species Gene trees Regulatory build (ENCODE) Variation display and VEP Display of user data BioMart (data export) Programmatic access via the APIs Completely Open Source
9 Access scales One by one Main browser Mobile site BioMart REST API VEP Groups Perl API MySQL FTP Whole genome
10 Vertebrate species on Ensembl
11 Non-vertebrates on Ensembl genomes Fungi Protists Bacteria Metazoa Plants
12 Ensembl and Ensembl Genomes Ensembl EnsemblGenomes Released Species Vertebrates (fly, worm and yeast as outgroups) Non-vertebrates (protists, plants, fungi, metazoa, bacteria) Annotation by Ensembl in collaboration with the scientific communities URL
13 Release cycle New/updated interfaces July May Updated regulation data New genome assemblies 2-3 months Updated variation data Compara on new genes and genomes Underlying software updates Updated gene sets
14 Ensembl Tools Tools allow: Interpretation and processing of your own data Custom download of Ensembl data for further analysis
15 BLAST/BLAT for sequence searching Find Ensembl sequences that match your sequence using BLAST/BLAT Search: Nucleotide sequences Protein sequences Short sequences (eg primers, morpholinos, sirnas) Search against Genomic sequences cdna sequences Protein sequences
16 Hands on BLAST/BLAT I ve designed a pair of primers for RT-PCR against human BRCA2 I want to make sure they don t have any non-specific hits that will mess up my RT-PCR results The sequences are: >fwd GAGGACTCCTTATGTCCAAATTT >rev GAGAATCAGCTTCTGGGGTAATAA
17 Assembly converter You have data mapped to an old genome assembly You want to update your data to map it to a new one
18 What is a genome assembly? Sequence reads CGGCCTTTGGGCTCCGCCTTCAGCTCAAGA CAGCTGTCCCAGATGAC ACTTAACTTCCCTCCCAGCTGTCC GGGCTCCGCCTTCAGCTC CGGCCTTTGGGCTCC TCCCAGCTGTCCCAGATGACGCCATC AACTTCCCTCCCAGCT CAGATGACGCC TCCGCCTTCAGCTCAAGACTTAACTTC Match up overlaps CGGCCTTTGGGCTCCGCCTTCAGCTCAAGA AACTTCCCTCCCAGCT CAGATGACGCC TCCGCCTTCAGCTCAAGACTTAACTTC TCCCAGCTGTCCCAGATGACGCCATC ACTTAACTTCCCTCCCAGCTGTCC GGGCTCCGCCTTCAGCTC CGGCCTTTGGGCTCC CAGCTGTCCCAGATGAC Genome assembly CGGCCTTTGGGCTCCGCCTTCAGCTCAAGACTTAACTTCCCTCCCAGCTGTCCCAGATGACGCCATC
19 Genome contigs BL102 AL476 BL AL CM553 CM IM768 IM
20 Reference alleles BL102 AL476 BL BL102 AGTCGTAGCTAGC TAGGCCATAGGCGA AL CM553 CM IM768 IM Frequency T = 0.05, frequency G = 0.95 G is the allele in all primates T causes disease susceptibility Perhaps G should be the reference allele? We can replace the region with a new contig
21 Genome Gaps BL102 BL102 AL476 AL476 BL Gap in the genome caused by: Poor sequencing at this region No contig was ever cloned AL CM553 CM IM768 IM We can fill in the gap with a new contig
22 Incorrectly assembled contigs BL102 BL102 CM553 AL476 BL BL CM AL CM553 AL476 IM768 IM768 AL CM IM IM
23 New genome assemblies Fixing errors in the genome produces a new genome assembly New genome assemblies mean re-mapping of all genome features Ensembl will stop updating the old assembly when a new one is brought in You ve got data mapped to the old assembly and you want to compare to the up-to-date Ensembl annotation
24 Assembly converter Converts genome coordinates to a different genome assembly. Works with: BED (simple coordinates) GFF (gene, transcript and exon coordinates) GTF (gene, transcript and exon coordinates) WIG (values plotted against the genome) VCF (variants)
25 Hands-on Assembly converter We re going to convert a small BED file from the human genome assembly GRCh37 to the more recent GRCh38 BED is a simple features format which lists the start and end coordinate of the feature P P P3
26 Data Slicer for variants Whole genome VCF files are unwieldy They contain all variants in the genome They contain all genotypes from all individuals studied Sometimes you just want to analyse a small region and one population The Data Slicer allows you to take a slice of a VCF and narrow down to only individuals and populations of interest Data Slicer currently only accesses the 1000 Genomes data It is only available for human and only on GRCh37
27 Hands on Data Slicer I want to get a VCF of the region containing the MC1R gene for the British population MC1R is found at 16: in GRCh37 The three-letter code for the British population in 1000 Genomes is GBR
28 FTP Files of our complete database: Genomic, cdna, CDS, ncrna and protein sequence (FASTA) Annotated sequence (EMBL, GenBank) Gene sets (GTF, GFF) Whole-genome multiple and gene-based multiple alignments (MAF) Variants (VCF, GVF) Constrained elements (BED) Regulatory features (BED, BigWig) RNA-Seq files (BAM, BigWig) MySQL database
29 Access FTP Your favourite FTP client FTP site ftp://ftp.ensembl.org/pub/ FTP downloads page
30 FTP files are big Multiple Mb/Gb Lots of time to download/unzip Do you really need this data? Make sure it s the right file before you download.
31 File chameleon for NGS analysis Although files on the Ensembl FTP site are in a standard format, different tools define the standards differently (sigh!) Your NGS analysis tool might need files that are slightly different to the Ensembl formats File chameleon allows you to download files with these adjustments
32 Hands on File Chameleon I need a GFF3 file of cat for my RNA-seq analysis. My tool requires: UCSC-style chromosome naming like chr1 Only genes shorter than 4 Mb Transcript IDs in every line We will use File Chameleon to download this customised file.
33 Analyse your own variants with the VEP Find out the effects of your own variants on Ensembl genes Analyse whole genome variant calls Filter variants to find those that might be interesting
34 Your own variant data Variant coordinates HGVS notation ENST :c.1047_1048insC 5:g T>C NM_ :c.7C>T ENSP :p.Ala2233Asp NP_ :p.Ile2285Val VCF #CHROM Variant IDs rs COSM rs FANCD1:c.475G>A rs POS ID rs rs /C T/C T/A G/C C/T REF ALT G A T A A G,T T.
35 Variation types 1) Small scale in one or few nucleotides of a gene Small insertions and deletions (DIPs or indels) Single nucleotide polymorphism (SNP) A G A C T T G A C C T G T C T - A A C T G G A T G A C T T G A C - T G T C T G A A C G G G A 2) Large scale in chromosomal structure (structural variation) Copy number variations (CNV) Large deletions/duplications, insertions, translocations deletion duplication insertion translocation
36 Variation consequences CODING Synonymous Regulatory CODING Non-synonymous AAAAAAA ATG 5 Upstream 5 UTR Splice site Intronic 3 UTR 3 Downstream
37 Consequence terms
38 Predicting missense effects SIFT and PolyPhen SIFT and PolyPhen score changes in amino acid sequence based on: How well conserved the protein is The chemical change in the amino acid 3D structure and domains (PolyPhen only) SIFT and PolyPhen are predictions, not facts A prediction will never be as good as experimental validation
39 SIFT 1 PolyPhen Probably damaging Possibly damaging Tolerated Benign Deleterious 0
40 Use the VEP
41 Species that work with the VEP? + everything in Plants, Fungi, Metazoa, Protists and Bacteria
42 Set up a cache - Speed up your VEP script with an offline cache. - Use prebuilt caches for Ensembl species. - Or make your own from GTF and FASTA files even for genomes not in Ensembl.
43 VEP plugins Plugins add extra functionality to the VEP They may extend, filter or manipulate the output of the VEP. Plugins may make use of external data or code. Available on the web tool and with the script.
44 Hands on We re going to look at a set of four variants to find out what genes they hit and what effect they have on them A/- + var C/A + var C/G + var G/A + var4
45 Questions? We ve muted all the mics Ask questions in the Chat box in the webinar interface I will check the Chat interface There s no threading so please respond
46 Host an Ensembl course Browser course We can teach an Ensembl course at your institute for free (except ½-2 day course on the Ensembl browser, aimed trainers expenses). at wet-lab scientists. us: One trainer. REST API course 1-2 day course on the Ensembl Perl API, aimed at bioinformaticians. 1-2 trainers.
47 Help and documentation Course online Tutorials Flash animations us Ensembl public mailing lists
48 Follow us
49 Publications Aken, B. et al Ensembl 2017 Nucleic Acids Research Xosé M. Fernández-Suárez and Michael K. Schuster Using the Ensembl Genome Server to Browse Genomic Sequence Data. Current Protocols in Bioinformatics (2010) Giulietta M Spudich and Xosé M Fernández-Suárez Touring Ensembl: A practical guide to genome browsing BMC Genomics 11:295 (2010)
50 Ensembl Acknowledgements The Entire Ensembl Team Funding Co-funded by the European Union
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